I don't think it is surprising that we have to simplify ideas in threads like these, but your criticisms are always welcomed and appreciated.
The context of the paragraph you quoted is found in a subsequent post where I discussed the debate between Rationalism and Empiricism. I will fully agree that hypotheses often start as an idea born of human intuition, but it doesn't stop there in science. Previously, it did stop there. That was the big shift that happened during the birth of modern science. No longer did natural philosophers argue about how nature worked using the methods of Aristotle. Rather, they required empirical evidence to back their arguments, and they also required their ideas to be falsifiable. If I were to simplify again, the scientific method boils down to the ethos of trying to prove yourself wrong through experiments.
When atheists mention Geocentrism it is usually within the context of the Roman Catholic Church persecuting those who challenged it because it went against religious orthodoxy, and it is often used as analogy for Young Earth Creationism.
One example I personally enjoy is the lumeniferous aether, or the ether as it was later called. They discovered that light acted as a wave, so human intuition said that there had to be something that was waving, a medium through these waves interacted with. Michelson and Morley set up an experiment to measure the ether, and it just wasn't there. Many people argued against their findings, but over time the evidence demonstrated that there was no ether. In the age of Rationalism, the ether might have stood.